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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGACTATTGGCATTGATTTTCTTTCAAAAACAATGTACCTTGAAGACCGCACCGTGCGGCTACAGCTTTGgtaactttctaagaatcattatgtgatttagcaacattatgcaaattcgcctcgttctgcaactttcctcgttttactctgtaccttcaaacaatctgtg...

Basic information

species Physcomitrella patens
transcript PP1S12_267V6.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S12_267V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: LOC_Os03g09140.1 (Oryza sativa), 5'ss of exon 2
GCGACTATTGGCATTGATTTTCTTTCAAAAACAATGTACCTTGAAGACCGCACCGTGCGGCTACAGCTTTGgtaact----ttctaagaa---tcattatgtgatttagcaacattatgcaaattcgcctcgttctgcaactttcctcgttttactctgtaccttcaaacaatctgtg
||||| || || || ||||| || || || || |||||||| |||||||| ||||| ||||| ||||||||||| ||    |||| | ||   ||  | | || |||  |   || || || | ||  ||  |     | |||  |  | ||       | |  |      | ||   
GCGACGATCGGGATCGATTTCCTCTCCAAGACGATGTACCTCGAAGACCGAACCGTACGGCTGCAGCTTTGgtatctgagattctgaaaactctctctctttgtttttcccctatcat-catactctgcttatca---agcttgtcctgcttacgagaattcagttggtgcagct---

upper sequence: PP1S12_267V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G128771_T01 (Zea mays), 5'ss of exon 2
GCGACTATTGGCATTGATTTTCTTTCAAAAACAATGTACCTTGAAGACCGCACCGTGCGGCTACAGCTTTGgtaactttctaagaatcattatgtgatttagcaacattatgcaaattcgcctcgttctgcaactttcctcgttttactctgtaccttcaaacaa-tctgtg----
|| || ||||||||||| ||||| |||||||||||||| || |||||||| || || ||  |||| || |||||| | ||    |||| ||   |  |     |    ||| | |       | |||| |  |   |  | |||| | |   ||  |    || | |  |||    
GCAACGATTGGCATTGACTTTCTGTCAAAAACAATGTATCTAGAAGACCGAACTGTACGTTTACAACTCTGgtaagtatc----aatctttggtttgtccctaattcatatacgagcgtagttggttcagtcatagtgat-gtttaaatgattaaatcagtactacttcgtgatgc

upper sequence: PP1S12_267V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G075719_T01 (Zea mays), 5'ss of exon 2
GCGACTATTGGCATTGATTTTCTTTCAAAAACAATGTACCTTGAAGACCGCACCGTGCGGCTACAGCTTTGgta-actttcta-----agaatcattatgtgatttagcaacattatgcaaattcgcctcgttctgcaactttcctcgttttactctgtaccttcaaacaatctgtg
|| || ||||| |||||||| || ||||| |||||||||||||||||  | || ||| | || || || ||||| | || |||       |  | |||     | | ||  |||| || |  | ||   ||||     || ||   | | |     | |   | ||           
GCTACAATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtataattactactactgcatccgttagcctgtatggccccattgtg-atctacggaccgtt----gaccttatgcatgtgttgttttctttgcag----------

upper sequence: PP1S12_267V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G169694_T01 (Zea mays), 5'ss of exon 2
GCGACTATTGGCATTGATTTTCTTTCAAAAACAATGTACCTTGAAGACCGCACCGTGCGGCTACAGCTTTGgta-actttctaagaatcattatgtgatttagcaacattatgcaaattcgcctcgttctgcaactttcctcgttttactctgtaccttcaaacaatctgtg
|| || ||||| |||||||| || ||||| |||||||||||||||||  | || ||| | || || || |||||   |  |||  | |   |   |    |     |    || | ||        |  ||    | | |  |||||| | | |   | ||           
GCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtatggtgactactactgcattcatagcctgtttgccccttg-agatctatggactgttgaccttatgcatgttttattttct--ttgcag----------

upper sequence: PP1S12_267V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA08G14390.1 (Glycine max), 5'ss of exon 2
GCGACTATTGGCATTGATTTTCTTTCAAAAACAATGTACCTTGAAGACCGCACCGTGCGGCTACAGCTTTGgtaa-------ctttctaagaatcat-tatgtga-tttagcaacattatgcaaattcgcct--cgttctgcaactttcct------cgttttactc-tgtacctt-caaacaatctgtg----------------------------------------
|| |||||||| ||||| ||| | |||||||||||||||||||||||  | || || ||  | |||||||||||           |||   |||||| |||   |  | ||     ||||     || |  |    |||  ||| | |  |      |   || ||  | | |||   |  || | | |                                         
GCAACTATTGGTATTGACTTTTTGTCAAAAACAATGTACCTTGAAGATAGAACTGTTCGCTTGCAGCTTTGgtaggatgaattcctcttcaaatcatatatacaagctcagtctttttatatttgtttgtttatttttcaacaattatattagagtgcacattgctggtatgcctagtaggcattgtttatttttacaatttctgagcttagtatatgttaacttcacag

upper sequence: PP1S12_267V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA05G31200.1 (Glycine max), 5'ss of exon 2
GCGACTATTGGCATTGATTTTCTTTCAAAAACAATGTACCTTGAAGACCGCACCGTGCGGCTACAGCTTTGgtaa------ctttctaagaatcatta-tgtgatttagcaacattatgcaaattcgcctcgttctgcaactttcct---------cgttttactc-tgtacctt-caaacaatctgtg----------------------------------------
|| |||||||| ||||| ||| | |||||||||||||||||||||||  | || || || || |||||||||||          |||   |||||| | |   |  |  ||    |||  | ||| |  |  || | ||||  |  |         |   || ||  |   ||||  |  || ||| |                                         
GCAACTATTGGTATTGACTTTTTGTCAAAAACAATGTACCTTGAAGATAGAACTGTTCGCCTGCAGCTTTGgtaggatgactcctcttcaaatcataaatacaagct--cagt-ctatttatatttgttttatttttcaacaattatattagagtacacattgctggtacgccttataggcactctttattcttacaatttctgagcttagtatatgttaacttcacag

upper sequence: PP1S12_267V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA18G02040.1 (Glycine max), 5'ss of exon 2
GCGACTATTGGCATTGATTTTCTTTCAAAAACAATGTACCTTGAAGACCGCACCGTGCGGCTACAGCTTTGgtaactttctaagaatcattatgtgatttagcaacat-tatgcaaattcgcctcgttctgcaactttcctcg--ttttactctgtaccttcaaacaatctgtg------------------------------------------------
|| |||||||| ||||| ||  | ||||||||||||||||||||||| || || || || || |||||||||||      ||    || |||  | ||    ||| |  |||  | |||    |  ||||  || ||   |    ||| ||  |||   |  |  || | | |                                                 
GCTACTATTGGTATTGACTTCTTGTCAAAAACAATGTACCTTGAAGATCGAACAGTTCGTCTGCAGCTTTGgtaggcca-tattcctctttaactcatgccacaagacctatttatattttttt--ttctaaaagttatattagatttcacattgt-tgtgtaggcactttttttaacccattctttgtatgttaaaattgtttcatattttaacttcacag

upper sequence: PP1S12_267V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA01G41100.1 (Glycine max), 5'ss of exon 2
GCGACTATTGGCATTGATTTTCTTTCAAAAACAATGTACCTTGAAGACCGCACCGTGCGGCTACAGCTTTGgtaactttctaagaatcattatgtgatttagcaacattatgcaaattcgcctcgttctgcaactttcctcgttttactctgtaccttcaaacaatctgtg----
|| || ||||| ||||||||||| |||||||| ||||| |||||||| || || || || || ||| | ||||||  |     | | ||  || | ||  || || | |||  |   |    | ||   | ||        ||||||         |  ||  | |  |      
GCTACAATTGGTATTGATTTTCTATCAAAAACTATGTATCTTGAAGATCGAACTGTTCGACTGCAGTTGTGgtaagatat--gggaccagcatctcat--agtaatagtataaattataaaatggtcaggaaatgaaaagggttttaggaaaggattggaagaagtaggatcatg

upper sequence: PP1S12_267V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: AT2G44610.1 (Arabidopsis thaliana), 5'ss of exon 2
GCGACTATTGGCATTGATTTTCTTTCAAAAACAATGTACCTTGAAGACCGCACCGTGCGGCTACAGCTTTGgtaactttctaagaatcattatgtgatttagcaacattatgcaaattcgcctcgttctgcaactttcctcgttttactctgtaccttcaaacaatctgtg--
|| || ||||| ||||||||||| ||||| ||||||||||||||||| || || ||  | || ||| | ||||||  |  | ||  || ||     ||||   || | |  | | | |  | | |     ||  |||    | || ||   |       |||  || ||    
GCCACAATTGGTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCGAACGGTCAGACTTCAGTTGTGgtaagatcttgagcctcttt---caattttcgaatact--gaagaataacattgcagatcattttttgatgattaacatcgagagccgaaatcatatgacag

upper sequence: PP1S12_267V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: AT5G10260.1 (Arabidopsis thaliana), 5'ss of exon 2
GCGACTATTGGCATTGATTTTCTTTCAAAAACAATGTACCTTGAAGACCGCACCGTGCGGCTACAGCTTTGgtaacttt-ctaagaatcattatgtgatttagc--aacattatgcaaattcgcctcgttctgcaactttcctcgtttta-ctctgtaccttcaaacaatctgtg
|| || ||||| ||||||||| | |||||||||||||||||||| ||  | || || || || || || |||||| |    | |  ||  |  | |  |||     || | | | ||  ||   |   |  |  | ||      |  | | || | |   ||   | ||| |   
GCAACCATTGGAATTGATTTTTTGTCAAAAACAATGTACCTTGAGGATAGGACTGTTCGTCTCCAACTATGgtaattcaattcaatatgctcctatcttttgatctaaaacttttcacctttatcaaata-tatatctagatgagcataatctttattgtttggtataatgt---

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|162197427|gb|FC372805.1|FC372805
EST:     CTTTCAAAAACAATGTACCTTGAAGACCGCACCGTGCGGCTACAGCTTTG                         GGATACCGCAGGACAAGAAAGATTCCGGAGTCTAATTCCCAGCTATATCCG
genomic: CTTTCAAAAACAATGTACCTTGAAGACCGCACCGTGCGGCTACAGCTTTGgtaactttct ... gtggttacagGGATACCGCAGGACAAGAAAGATTCCGGAGTCTAATTCCCAGCTATATCCG
EST: gi|100364148|gb|BY966739.1|BY966739
EST:     CTTTCAAAAACAATGTACCTTGAAGACCGCACCGTGCGGCTACAGCTTTG                         GGATACCGCAGGACAAGAAAGATTCCGGAGTCTAATTCCCAGCTATATCCG
genomic: CTTTCAAAAACAATGTACCTTGAAGACCGCACCGTGCGGCTACAGCTTTGgtaactttct ... gtggttacagGGATACCGCAGGACAAGAAAGATTCCGGAGTCTAATTCCCAGCTATATCCG
EST: gi|162171600|gb|FC347541.1|FC347541
EST:     CTTTCAAAAACAATGTACCTTGAAGACCGCACCGTGCGGCTACAGCTTTG                         GGATACCGCAGGACAAGAAAGA
genomic: CTTTCAAAAACAATGTACCTTGAAGACCGCACCGTGCGGCTACAGCTTTGgtaactttct ... gtggttacagGGATACCGCAGGACAAGAAAGA
EST: gi|100445813|gb|CJ970112.1|CJ970112
EST:     CTTTCAAAAACAATGTACCTTGAAGACCGCACCGTGCGGCTACAGCTTTG                         GGATACCGCAGGACAAGAAAGATTCCGGAGTCTAATTCCCAGCTATATCCG
genomic: CTTTCAAAAACAATGTACCTTGAAGACCGCACCGTGCGGCTACAGCTTTGgtaactttct ... gtggttacagGGATACCGCAGGACAAGAAAGATTCCGGAGTCTAATTCCCAGCTATATCCG
EST: gi|208387491|gb|DC933354.1|DC933354
EST:     CTTTCAAAAACAATGTACCTTGAAGACCGCACCGTGCGGCTACAGCTTTG                         GGATACCGCAGGACAAGAAAGATTCCGGAGTCTAATTCCCAGCTATATCCG
genomic: CTTTCAAAAACAATGTACCTTGAAGACCGCACCGTGCGGCTACAGCTTTGgtaactttct ... gtggttacagGGATACCGCAGGACAAGAAAGATTCCGGAGTCTAATTCCCAGCTATATCCG

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGACTATTGGCATTGATTTTCTTTCAAAAACAATGTACCTTGAAGACCGCACCGTGCGGCTACAGCTTTGgtaactttctaagaatcattatgtgatttagcaacattatgcaaattcgcctcgttctgcaactttcctcgttttactctgtaccttcaaacaatctgtg

- - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - -  TGAAGA